norm.quantile {ENmix} | R Documentation

## Quantile normalization.

### Description

Quantile normalization of methylation intensity data across samples for Illumina Infinium HumanMethylation 450 and MethylationEPIC BeadChip.

### Usage

    norm.quantile(mdat, method = "quantile1")

### Arguments

`mdat` | An object of class `methDataSet` or `MethylSet`.
`method` | Quantile normalization method: "quantile1", "quantile2", or "quantile3".

### Details

By default, method = "quantile1", which will separately quantile normalize Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile2" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile3" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I and II probes together.

### Value

The output is an an object of class `methDataSet` or `MethylSet`.

### Author(s)

Zongli Xu

### References

Pidsley, R., CC, Y.W., Volta, M., Lunnon, K., Mill, J. and Schalkwyk, L.C. (2013) A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics, 14, 293.

### Examples

    #for methDataSet
    path <- file.path(find.package("minfiData"),"extdata")
    rgSet <- readidat(path = path,recursive = TRUE)
    mdat<-preprocessENmix(rgSet, bgParaEst="oob",nCores=6)
    mdatq<-norm.quantile(mdat, method="quantile1")

    #for MethySet
    if (require(minfiData)) {
    mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
    mdatq=norm.quantile(mdat,method="quantile1")
    }

[Package ENmix version 1.30.03 Index]